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Molecule Parameter List for AI-1 | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Quorum_
repressilator | 69 | Network |
Shared_Object_Quorum_repressilator, TetR, LacI,
Lambda-cl, LacI_2nd_copy, LuxI | This model represents a single cell with the repressilator circuit, which is part of a population of similar cells. The repressilator circuit is a network of three proteins, i.e. LacI, TetR, Lambda-cI.
The single repressilator model is at accession number 68 in the DOQCS database.
In the current model, the LacI is coupled with LuxI which forms an Autoinducer(AI) protein, which couples to LuxR which activates LacI. The AI protein difffuses across the cell membrane so that the population of cells can interact. The lifetime ratio is the ratio between the mRNA and protein lifetimes. This ratio in different cells is chosen from a random gaussian distribution of mean 1 and standard deviation 0.05. The lifetime ratio of this example cell is 0.9837 |
AI-1 acting as a Molecule in Quorum_repressilator Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | AI-1 | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 0 | 3 | No | | AI translated from luxI m-RNA Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator by Elowitz, M. et al. (2000) Nature 403:335-338 |
AI-1 acting as a Substrate in a reaction in Quorum_repressilator Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| | Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | 1 | AI_degradation | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 0.2
(s^-1) | 0
(s^-1) | - | - | Substrate
AI-1
Product
Degraded_AI
| | | Degradation of autoinducer. kf = 0.2, McMillen et al (2002) PNAS 99(2): 679-84 | | 2 | LuxR_binding_
autoinducer | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 5
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.02(uM) | - | Substrate
AI-1
LuxR
Product
LuxR-AI
| | | Binding of Lux R to the autoinducer protein Kf = 5e+06 /M = 5 /uM McMillen, M. et al. (2002) PNAS USA 99(2): 679-84 | | 3 | AI_diffusion | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 2
(s^-1) | 2
(s^-1) | Keq = 1(uM) | 0.25sec | Substrate
AI-1
Product
AI-extracellular
| | | Diffusion of the autoinducer from inside the cell to the outside and vice versa. Garcia-Ojalvo, J et al. (2004) PNAS USA 101(30):10955-10960 |
AI-1 acting as a Product in a reaction in Quorum_repressilator Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | AI_form | Quorum_
repressilator
Accession No. : 69 | LuxI
Pathway No. : 303 | 0.01
(s^-1) | 0
(s^-1) | - | - | Substrate
LuxI
Product
AI-1
| | Formation of Autoinducer The forward rate has taken from PNAS 101: 10955-60 by Garcia & Elowitz et al (2004) |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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